[gmx-users] Atom MNZ1 in residue LYS 107 was not found

[Steven Neumann]

Thankl you.
Well... Indeed, just removed them manually and everything is ok.

Steven

On Mon, Apr 16, 2012 at 2:38 PM, Peter C. Lai <pcl at uab.edu> wrote:

> Sounds like a bad VMD selection that didn't remove MNZ1 when you did the
> conversion. MNZ1 sounds like a virtual site for the extra hydrogen off NZ
> in protonated LYS.
>
> On 2012-04-16 02:32:09PM +0100, Steven Neumann wrote:
> > Dear Gmx Users,
> >
> > I run implicit simulation for 1 us with virtual sites on hydrogens, then
> > using VMD extracted coordinates into the pdb file. As I want to run
> > explicit solvent simulation now I removed hydrogens so that pdb2gmx will
> > add them. Then I got an error while trying to pdb2gmx using Charmm27:
> >
> > Atom MNZ1 in residue LYS 107 was not found in rtp entry LYS with 22 atoms
> > while sorting atoms.
> >
> > How come this atom appears in my pdb file? Any suggestions?
> >
> > Thank you,
> >
> > Steven
>
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> ==================================================================
> Peter C. Lai                    | University of Alabama-Birmingham
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